Merge remote-tracking branch 'upstream/master' into docbookfive

* upstream/master: Change location of some fields in the entry editor (#4448) Bump applicationinsights-core from 2.2.0 to 2.2.1 (#4488) Added feature to add server timezone when connecting to shared database (#4483) Bump applicationinsights-logging-log4j2 from 2.2.0 to 2.2.1 (#4487) fix save button Update archunit from 0.9.1 -> 0.9.2 Fix move to group always moves first entry (#4457) Add eprint cleanup (#4445) respect preference state (#4468) Set auto-update checkbox enable/disable when reading preferences (#4446) Improve MathSciNet fetcher and add ISBN fetcher to entry editor toolbar (#4444) New translations JabRef_en.properties (German) (#4455) New Crowdin translations (#4454) Fix error in l10n file: Toogle -> Toggle (#4453) Remove depandabot
JabRef · Nov 17, 2018 · c169517 · c169517
2 parents 020a03f + 2953849
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -11,11 +11,19 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 ## [Unreleased]
 
 ### Changed
+- We changed the location of some fields in the entry editor (you might need to reset your preferences for these changes to come into effect)
+  - Journal/Year/Month in biblatex mode -> Deprecated (if filled)
+  - DOI/URL: General -> Optional
+  - Internal fields like ranking, read status and priority: Other -> General
+  - Moreover, empty deprecated fields are no longer shown
+- Added server timezone parameter when connecting to a shared database.
 - We updated the dialog for setting up general fields.
 - URL field formatting is updated. All whitespace chars, located at the beginning/ending of the url, are trimmed automatically
 - We changed the behavior of the field formatting dialog such that the `bibtexkey` is not changed when formatting all fields or all text fields.
 - We added a "Move file to file directory and rename file" option for simultaneously moving and renaming of document file. [#4166](https://github.com/JabRef/jabref/issues/4166)
 - Use integrated graphics card instead of discrete on macOS [#4070](https://github.com/JabRef/jabref/issues/4070)
+- We added a cleanup operation that detects an arXiv identifier in the note, journal or url field and moves it to the `eprint` field.
+  Because of this change, the last-used cleanup operations were reset.
 - We changed the minimum required version of Java to 1.8.0_171, as this is the latest release for which the automatic Java update works.  [4093](https://github.com/JabRef/jabref/issues/4093)
 - The special fields like `Printed` and `Read status` now show gray icons when the row is hovered.
 - We added a button in the tab header which allows you to close the database with one click. https://github.com/JabRef/jabref/issues/494
@@ -28,6 +36,8 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We changed the default keyboard shortcuts for moving between entries when the entry editor is active to ̀<kbd>alt</kbd> + <kbd>up/down</kbd>.
 - Opening a new file now prompts the directory of the currently selected file, instead of the directory of the last opened file.
 - Window state is saved on close and restored on start.
+- We made the MathSciNet fetcher more reliable.
+- We added the ISBN fetcher to the list of fetcher available under "Update with bibliographic information from the web" in the entry editor toolbar.
 - Files without a defined external file type are now directly opened with the default application of the operating system
 - We streamlined the process to rename and move files by removing the confirmation dialogs.
 - We removed the redundant new lines of markings and wrapped the summary in the File annotation tab. [#3823](https://github.com/JabRef/jabref/issues/3823)
@@ -76,7 +86,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where the list of XMP Exclusion fields in the preferences was not be saved [#4072](https://github.com/JabRef/jabref/issues/4072)
 - We fixed an issue where the ArXiv Fetcher did not support HTTP URLs [koppor#328](https://github.com/koppor/jabref/issues/328)
 - We fixed an issue where only one PDF file could be imported [#4422](https://github.com/JabRef/jabref/issues/4422)
-
+- We fixed an issue where "Move to group" would always move the first entry in the library and not the selected [#4414](https://github.com/JabRef/jabref/issues/4414)
 
 
 

diff --git a/README.md b/README.md
@@ -2,7 +2,6 @@
 
 [![Build Status](https://travis-ci.org/JabRef/jabref.svg?branch=master)](https://travis-ci.org/JabRef/jabref)
 [![codecov.io](https://codecov.io/github/JabRef/jabref/coverage.svg?branch=master)](https://codecov.io/github/JabRef/jabref?branch=master)
-[![Dependabot Status](https://api.dependabot.com/badges/status?host=github&repo=JabRef/jabref)](https://dependabot.com)
 [![Donation](https://img.shields.io/badge/donate%20to-jabref-orange.svg)](https://donations.jabref.org)
 
 JabRef is an open-source, cross-platform citation and reference management tool licensed under the  [MIT license](https://tldrlegal.com/license/mit-license).

diff --git a/build.gradle b/build.gradle
@@ -157,8 +157,8 @@ dependencies {
 
     errorproneJavac 'com.google.errorprone:javac:1.8.0-u20'
 
-    compile group: 'com.microsoft.azure', name: 'applicationinsights-core', version: '2.2.0'
-    compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '2.2.0'
+    compile group: 'com.microsoft.azure', name: 'applicationinsights-core', version: '2.2.1'
+    compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '2.2.1'
 
     testImplementation 'org.junit.jupiter:junit-jupiter-api:5.3.1'
     testCompile 'org.junit.jupiter:junit-jupiter-params:5.3.1'
@@ -174,8 +174,8 @@ dependencies {
     testCompile 'org.reflections:reflections:0.9.11'
     testCompile 'org.xmlunit:xmlunit-core:2.6.2'
     testCompile 'org.xmlunit:xmlunit-matchers:2.6.2'
-    testCompile 'com.tngtech.archunit:archunit-junit5-api:0.9.1'
-    testRuntime 'com.tngtech.archunit:archunit-junit5-engine:0.9.1'
+    testCompile 'com.tngtech.archunit:archunit-junit5-api:0.9.2'
+    testRuntime 'com.tngtech.archunit:archunit-junit5-engine:0.9.2'
     testCompile "org.testfx:testfx-core:4.0.+"
     testCompile "org.testfx:testfx-junit5:4.0.+"
 

diff --git a/src/main/java/org/jabref/gui/actions/CleanupAction.java b/src/main/java/org/jabref/gui/actions/CleanupAction.java
@@ -10,7 +10,6 @@
 import org.jabref.gui.undo.NamedCompound;
 import org.jabref.gui.undo.UndoableFieldChange;
 import org.jabref.gui.util.BackgroundTask;
-import org.jabref.gui.util.DefaultTaskExecutor;
 import org.jabref.logic.cleanup.CleanupPreset;
 import org.jabref.logic.cleanup.CleanupWorker;
 import org.jabref.logic.l10n.Localization;
@@ -23,11 +22,6 @@ public class CleanupAction implements BaseAction {
     private final BasePanel panel;
     private final DialogService dialogService;
 
-    /**
-     * Global variable to count unsuccessful renames
-     */
-    private int unsuccessfulRenames;
-
     private boolean isCanceled;
     private int modifiedEntriesCount;
     private final JabRefPreferences preferences;
@@ -44,13 +38,31 @@ public void action() {
         if (isCanceled) {
             return;
         }
-        CleanupDialog cleanupDialog = new CleanupDialog(panel.getBibDatabaseContext(), preferences.getCleanupPreset());
+        CleanupDialog cleanupDialog = new CleanupDialog(panel.getBibDatabaseContext(), preferences.getCleanupPreset(), preferences.getFilePreferences());
 
         Optional<CleanupPreset> chosenPreset = cleanupDialog.showAndWait();
-        chosenPreset.ifPresent(cleanupPreset ->
-                BackgroundTask.wrap(() -> cleanup(cleanupPreset))
-                              .onSuccess(x -> showResults())
-                              .executeWith(Globals.TASK_EXECUTOR));
+
+        if (chosenPreset.isPresent()) {
+            if (chosenPreset.get().isRenamePDFActive() && preferences.getBoolean(JabRefPreferences.ASK_AUTO_NAMING_PDFS_AGAIN)) {
+                boolean confirmed = dialogService.showConfirmationDialogWithOptOutAndWait(Localization.lang("Autogenerate PDF Names"),
+                        Localization.lang("Auto-generating PDF-Names does not support undo. Continue?"),
+                        Localization.lang("Autogenerate PDF Names"),
+                        Localization.lang("Cancel"),
+                        Localization.lang("Disable this confirmation dialog"),
+                        optOut -> Globals.prefs.putBoolean(JabRefPreferences.ASK_AUTO_NAMING_PDFS_AGAIN, !optOut));
+
+                if (!confirmed) {
+                    isCanceled = true;
+                    return;
+                }
+            }
+
+            preferences.setCleanupPreset(chosenPreset.get());
+
+            BackgroundTask.wrap(() -> cleanup(chosenPreset.get()))
+                          .onSuccess(result -> showResults())
+                          .executeWith(Globals.TASK_EXECUTOR);
+        }
     }
 
     public void init() {
@@ -111,21 +123,6 @@ private void showResults() {
     private void cleanup(CleanupPreset cleanupPreset) {
         preferences.setCleanupPreset(cleanupPreset);
 
-        if (cleanupPreset.isRenamePDF() && preferences.getBoolean(JabRefPreferences.ASK_AUTO_NAMING_PDFS_AGAIN)) {
-
-            boolean confirmed = DefaultTaskExecutor.runInJavaFXThread(() -> dialogService.showConfirmationDialogWithOptOutAndWait(Localization.lang("Autogenerate PDF Names"),
-                    Localization.lang("Auto-generating PDF-Names does not support undo. Continue?"),
-                    Localization.lang("Autogenerate PDF Names"),
-                    Localization.lang("Cancel"),
-                    Localization.lang("Disable this confirmation dialog"),
-                    optOut -> Globals.prefs.putBoolean(JabRefPreferences.ASK_AUTO_NAMING_PDFS_AGAIN, !optOut)));
-
-            if (!confirmed) {
-                isCanceled = true;
-                return;
-            }
-        }
-
         for (BibEntry entry : panel.getSelectedEntries()) {
             // undo granularity is on entry level
             NamedCompound ce = new NamedCompound(Localization.lang("Cleanup entry"));

diff --git a/src/main/java/org/jabref/gui/cleanup/CleanupDialog.java b/src/main/java/org/jabref/gui/cleanup/CleanupDialog.java
@@ -6,15 +6,16 @@
 import org.jabref.logic.cleanup.CleanupPreset;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.database.BibDatabaseContext;
+import org.jabref.model.metadata.FilePreferences;
 
 public class CleanupDialog extends BaseDialog<CleanupPreset> {
 
-    public CleanupDialog(BibDatabaseContext databaseContext, CleanupPreset initialPreset) {
+    public CleanupDialog(BibDatabaseContext databaseContext, CleanupPreset initialPreset, FilePreferences filePreferences) {
         setTitle(Localization.lang("Cleanup entries"));
         getDialogPane().setPrefSize(600, 600);
         getDialogPane().getButtonTypes().setAll(ButtonType.OK, ButtonType.CANCEL);
 
-        CleanupPresetPanel presetPanel = new CleanupPresetPanel(databaseContext, initialPreset);
+        CleanupPresetPanel presetPanel = new CleanupPresetPanel(databaseContext, initialPreset, filePreferences);
         getDialogPane().setContent(presetPanel);
         setResultConverter(button -> {
             if (button == ButtonType.OK) {

diff --git a/src/main/java/org/jabref/gui/cleanup/CleanupPresetPanel.fxml b/src/main/java/org/jabref/gui/cleanup/CleanupPresetPanel.fxml
@@ -0,0 +1,33 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<?import javafx.geometry.Insets?>
+<?import javafx.scene.control.CheckBox?>
+<?import javafx.scene.control.Label?>
+<?import javafx.scene.layout.VBox?>
+<fx:root xmlns:fx="http://javafx.com/fxml/1" spacing="10.0" type="VBox" xmlns="http://javafx.com/javafx/8.0.121"
+         fx:controller="org.jabref.gui.cleanup.CleanupPresetPanel">
+
+    <CheckBox fx:id="cleanUpDOI" text="%Move DOIs from note and URL field to DOI field and remove http prefix"/>
+    <CheckBox fx:id="cleanUpEprint"
+              text="%Move preprint information from 'URL' and 'journal' field to the 'eprint' field"/>
+    <CheckBox fx:id="cleanUpISSN" text="%Reformat ISSN"/>
+    <CheckBox fx:id="cleanUpUpgradeExternalLinks"/>
+    <CheckBox fx:id="cleanUpMovePDF"/>
+    <CheckBox fx:id="cleanUpMakePathsRelative" text="%Make paths of linked files relative (if possible)"/>
+    <CheckBox fx:id="cleanUpRenamePDF" text="%Rename PDFs to given filename format pattern"/>
+    <VBox spacing="5.0">
+        <Label fx:id="cleanupRenamePDFLabel"/>
+        <CheckBox fx:id="cleanUpRenamePDFonlyRelativePaths" text="%Rename only PDFs having a relative path"/>
+        <VBox.margin>
+            <Insets left="40.0"/>
+        </VBox.margin>
+    </VBox>
+
+    <CheckBox fx:id="cleanUpBiblatex"
+              text="%Convert to biblatex format (for example, move the value of the 'journal' field to 'journaltitle')"/>
+    <CheckBox fx:id="cleanUpBibtex"
+              text="%Convert to BibTeX format (for example, move the value of the 'journaltitle' field to 'journal')"/>
+
+    <VBox fx:id="formatterContainer"/>
+
+</fx:root>